Biotechnology in the Classroom: Using Genomics & Proteomics to ...


Dec 14, 2012 (4 years and 6 months ago)


Biotechnology 101

Presented by Kristin Majda

Kristin Majda


BS Biology & Minor in Professional Writing, U.C. Santa Barbara (1997)

Single Subject Clear Credential with CLAD, Cal State Northridge (2005)

MS Biotechnology & MBA, Cal State Channel Islands (2009)


Technical Writer (1997

Ventura County High School Science Teacher (2001

Oxnard College Instructor: Biology, Microbiology (2010)

CIRM Grant Analyst at Cal State Channel Islands (present)

VP of Gold Coast Science Network (GCSN), Member of Operating
Council for the Discovery Center for Science and Technology,

Member of AAAS, CA PTA Officer

About the Presenter


This presentation intends to:

Introduce teachers to excellent resources for understanding and teaching
genetics and biotechnology (and their interconnection with molecular
and cellular biology, biochemistry, physiology, and evolution)

Provide a
very basic

introduction to the common biotechnologies
teachers may address in their courses

This workshop is NOT for individuals who already have a strong
understanding of biotechnology principles and are looking to
advance their knowledge.

Biotechnology 101


Why is it important to include biotechnology in the K
science curriculum?

Biotechnology combines disciplines like genetics, molecular biology,
biochemistry, embryology and cell biology; with applications in medicine,
agriculture, environmental science, materials science, bio
fuels, etc.

Jobs in the biotechnology sector are increasing and there is a critical need for
a vast range of skilled workers, from lab assistants to PhD researchers

Biology and chemistry teachers can use applications of biotechnology to
strongly engage student interest and stimulate student
directed investigation
and experimentation in their classrooms

Biotechnology is part of the CA science standards for high school biology,
but has applications to many standards across the sciences for all grade

Biotechnology 101



Atomic Structure

Chemical Bonds


Reaction Rates

Chemical Equilibrium

Acids and Bases

Organic Chemistry

& Biochemistry

Biotechnology 101


Cell Biology





Investigation & Experimentation

It is what you make of it,
biotechnology helps you
make it great!

The California Science Standards (High School)


What are the

trends in biotechnology education?

What are the

trends in biotechnology education?

What factors limit our ability to provide a solid
biotechnology foundation in grades K

Funding for equipment

Teacher Knowledge and Experience

Time: Class Time, Prep Time

Biotechnology 101




they engage students and enable them to
visualize microscopic and/or abstract principles

Simulated labs and demos are helpful, but
on labs



Fully engaging students

Truly learning how to use equipment and perform techniques

Truly understanding the process of scientific discovery (scientific method)

Developing critical thinking skills

Developing students who are ready to enter the workforce or continue on to
study meaningful science at a college or university

Integration of
technical reading and writing

through the use of

and other primary and secondary sources is

to developing
students who can understand the true process of science, manage their
own learning, evaluate scientific claims, communicate effectively, and
think critically

Biotechnology 101



presentation will focus on


and other
online resources

Excellent resources for
on labs

are available, but we will not have
time to look at these at this workshop

Amgen Bruce Wallace Biotechnology Lab Program

(Website includes links to many great biotech education lab support
organizations in California)

The Exploratorium (make your own equipment)

Rad and other vendors have excellent resources and materials
and will help train you

Science Literacy

How Do Scientists Communicate?

Presented by Kristin Majda

Sunday, 9:20 a.m., Room 211

Biotechnology 101

Resources for Teaching Genetics


resources for understanding genetics are available from Cold
Spring Harbor’s online
DNA Learning Center (DNALC)


is at the heart of
, which aims to:

Develop therapies for genetic disorders, cancers, and other diseases in which
genetics plays a contributing role

Develop tissues for medical and research purposes (cloning, stem cells, tissue

Use genetic profiles to differentiate among individuals and diagnose diseases

Enhance plants and other living organisms with useful genes

Understand the evolutionary history and relationships between species and
within species, both modern and extinct

Biotechnology 101

Resources for Teaching Genetics

Genetics and molecular biology involve abstract concepts

The DNA Learning Center (DNALC) includes



Interactive websites

Curriculum development tools

Thematic lessons/units

Reference material

Biotechnology 101

Biotechnology 101

time animations of
transcription, translation,
DNA replication, and many


Many are downloadable

alone websites with
excellent resources for teaching
genetics and cellular and
molecular biology

Resources for Teaching Genetics

Genetic Basics (NIH Publication No. 01

Free Guide from
National Institutes of Health.

The Genes We Share with Yeast, Flies, Worms, and Mice

guide from the Howard Hughes Medical Institute, Office of
Communications, 4000 Jones Bridge Road, Chevy Chase, Maryland,

Bruce Wallace Biotechnology Lab Program

Amgen Foundation
provides all materials and equipment (including reagents) for eight
comprehensive biotechnology labs.

Human Genome Project

Biotechnology in the Classroom

Resources for Teaching Genomics


is the study of an organism's genome (entire set of genes)

Human Genome Project

is an international effort to map the entire
human genome based on DNA samples taken from a small group of
anonymous donors

The project began in 1990, rough draft of human genome announced in
2000, essentially complete genome was published in 2003 (two years early)

Broke the genome into segments approx. 150,000 base pairs long and then
ligated each segment into genetically engineered bacterial chromosomes
called BACs (bacterial artificial chromosomes). Inserted these vectors into
bacteria to amplify (make copies of) the DNA segments and then used
shotgun sequencing to determine the nucleotide sequence of each segment

Biotechnology 101

Resources for Teaching Genomics

What have we learned from the Human Genome Project?

The human genome contains 3.3 billion base pairs

(If expressed in units of computer data storage at 2 bits per base pair, there
would be 786 megabytes of raw data, which would be comparable to a fully
data loaded CD)

Almost all (99.9%) nucleotide bases are exactly the same in all people.

The human genome is estimated to contain 30,000 genes (much lower
than previous estimates of 80,000

140,000 genes).

Chromosome 1 has the most genes (2968), and the Y chromosome has
the fewest (231).

The average gene consists of 3000 bases, but sizes vary greatly, with
the largest known human gene being dystrophin at 2.4 million bases.

The functions are unknown for over 50% of discovered genes.

Biotechnology 101

Resources for Teaching Genomics

What have we learned from the Human Genome Project?

Genes appear to be concentrated in random areas along the genome,
with vast expanses of noncoding DNA between (other organisms'
genomes are more uniform, with genes evenly spaced throughout)

Stretches of up to 30,000 C and G bases repeating over and over often
occur adjacent to gene
rich areas, forming a barrier between the genes
and the "junk DNA." These CpG islands are believed to help regulate
gene activity.

Less than 2% of the genome codes for proteins.

Despite having more non
coding regions of DNA, humans have on
average three times as many kinds of proteins as the fly or worm
because of "alternative splicing" and chemical modifications to the
proteins resulting in the ability to produce different protein products
from the same gene.

Biotechnology 101

Resources for Teaching Genomics

Future goals of the Human Genome Project

Determine the function of all of genes

Identify all Single Nucleotide Polymorphisms (SNPs) and map them to
human diseases

Biotechnology 101

“The avalanche of genome data grows daily. The new challenge will be to use
this vast reservoir of data to explore how DNA and proteins work with each
other and the environment to create complex, dynamic living systems. Deriving
meaningful knowledge from the DNA sequence will define research through the
coming decades to inform our understanding of biological systems. This
enormous task will require the expertise and creativity of tens of thousands of
scientists from varied disciplines in both the public and private sectors
worldwide. Systematic studies of functional genomics will be the focus of
biological explorations in this century and beyond.”

Resources for Teaching Bioinformatics

Biotechnology 101


is the computational branch of molecular biology that
seeks to organize and make sense of all the genetic data being uncovered
(i.e. genomic sequences)

Determine the location of genes on chromosomes, start and stop sites

Predict the structure and function of resulting proteins

Classify genes/proteins into families

Determine evolutionary relationships between genes/proteins

Determine molecular interactions within proteins and between two or
more proteins

Determine/design potential receptors or ligands

Resources for Teaching Bioinformatics

Bioinformatics and the Human Genome Project

Excellent explanations of

Bioinformatics principles,

tools, and techniques

Five progressive Lessons

Copyright allows

reproduction for

educational uses

Biotechnology 101

Resources for Teaching Bioinformatics

Bioinformatics and the Human Genome Project

Lessons are supported

by a fictitious business

website that engages

students with role play

Biotechnology 101

Resources for Teaching Bioinformatics

Bioinformatics and the Human Genome Project

Biotechnology 101

Resources for Teaching Bioinformatics

Bioinformatics and the Human Genome Project

Biotechnology 101

Resources for Teaching Bioinformatics

Bioinformatics and the Human Genome Project

Biotechnology 101

Resources for Teaching Bioinformatics

Bioinformatics and the Human Genome Project

Biotechnology 101

Resources for Teaching Bioinformatics

Bioinformatics and the Human Genome Project

Biotechnology 101

Resources for Teaching Bioinformatics


to visualize small molecules and macromolecules in 3D.

Protein Data Bank
is a database that includes structural and
functional information about proteins, including the FASTA files
needed to display them in PyMOL.


is a simple tool for molecular visualization that has an online
gallery for easy access, with limited control over the appearance of

Biomolecular Explorer 3D

provides information about and 3D
images of relevent biological macromolecules right on the website.

provides analyses protein you input and predicts

Biotechnology in the Classroom

Resources for Teaching Bioinformatics


includes links to full text journal articles and other related


protein database.

SDSC Biology Workbench

allows scientists to search many protein
and nucleic acid sequence databases.


(Comprehensive Microbial Resource) maintains
databases that include prokaryotic, plant, fungal, and parasitic

ORF Finder

scans a FASTA sequence for a segment of DNA to
determine potential open reading frames (sections that code for a

Biotechnology in the Classroom

Resources for Teaching Bioinformatics

Proteomics Tools

Glycan Structure Database

Lipid bank

3D Molecular Designs


Lends out molecular models for 2 weeks

Biotechnology in the Classroom

Resources for Teaching Bioinformatics

Fold it

Protein folding game (

Biotechnology in the Classroom

More Free Tools & Resources

ELISA Tutorials/Animations


Pregnancy Test Animation

use this website and a pregnancy test from the Dollar
Store to show your kids how antibodies are used to identify proteins in body fluids like
blood and urine

Microarray Tutorial/Animations

PCR Tutorial/Animation

DNA Sequencing Tutorial/Animation

Biotechnology in the Classroom

More Free Tools & Resources

Recombinant DNA Tutorial/Animation

Stem Cells

Gel Electrophoresis Tutorial/Animation

Exploratorium Teacher Institute

4 week program in summer that teaches how to
make all kinds of “do it yourself” activities

(email or call 415

McGraw Hill’s Biotechnology Animations


Biotechnology in the Classroom

Biotechnologies for Your Classroom

Genetic Engineering

Recombinant DNA

Cellular Transformation

Gene Therapy

DNA Amplification

(PCR Method)

Separating and Identifying DNA

Gel Electrophoresis

DNA Sequencing

(Sanger Method)

DNA Microarrays



Biotechnology 101


Immunoassays (ELISA)

Creating 3D Proteins

Protein Folding

Stem Cell Technology


RNAi (gene silencing)



Thank You for Coming

Kristin Majda

Biotechnology in the Classroom

Biotechnologies for Your Classroom

include methods to:

Cut (restriction enzymes), paste (ligation), and move DNA segments from one
chromosome to another (recombinant DNA) and/or one cell to another (transformation)
(Genetic Engineering)

Make many copies of DNA segments (amplification)

Identify individuals and/or diseases based on their unique DNA profiles (DNA
sequencing, DNA fingerprinting, immunoassays, bioinformatics)

Determine evolutionary relationships (phylogenetics) within and between species

Turn genes up (upregulation) and down (down regulation), or on (gene activation) and
off (gene silencing)

Grow cells (cell culture), manipulate stem cells to develop into specific tissue types
(differentiation), or manipulate differentiated cells to regress back to stem cells

Create genetically identical copies of organisms (cloning)

Biotechnology 101